Captain Kohli made 123 out of 95 balls before he was bowled by Adam Zampa, leaving the hosts.
India lost their last four wickets for 62 runs to be bowled out for 281 now lead 2-1 at the five-match series.
The opener made 104 off 113 balls, putting on 193 for the first wicket with captain Aaron Finch, who had been dismissed lbw for 9-3 by left-arm wrist-spinner Kuldeep Yadav (3-64).
After ball tracking appeared to show the ball to where it landed pitching in a 20, finch was ineffective in reviewing your decision.
Glenn Maxwell (47), Marcus Stoinis (31 not out) and Alex Carey (21 not out) took the tourists for their first score of 300 or even more since June.
India slipped into 27-3 in reply and so were 86-4 when leg spinner Zampa (3-70) bowled MS Dhoni for 26.
Kedar Jadhav then wear 88 with Kohli before he was out lbw for 26, additionally disregarded by Zampa.
Kohli struck 16 fours and one six spinning pitch to maintain India in.
When batting second, kohli has hit 25 ODI centuries and that was the fourth time he has achieved in conquer.
The fourth ODI in Mohali begins at 08:00 GMT on Sunday.